The changes in reproductive strategies in response to environmental change, comparing the spatial niche and neutral cases.

<p>The spatial heterogeneity is fixed at <i>k = </i>16, and the white boxplot represent the spatial niche case and the grey boxplots represent the neutral case. Panel (a) represents the case in which frequency of environmental change is high, i.e., <i>p = </i>0.1, and panel (b) represents the case of low frequency of environmental change (<i>p = </i>0.01). Within each panel, the difference of the magnitude of environmental change is illustrated: <i>q = </i>0.1 at the top, <i>q = </i>0.01 in the middle, and <i>q</i> = 0 at the bottom. When <i>q = </i>0, it is identical to <i>p = </i>0, because it means there is no environmental change.</p

The frequency distributions of reproductive strategies in both the spatial niche and the neutral cases.

<p>The frequency of environmental change is fixed at <i>q = </i>0.1. The left side panels (a–c) represent the spatial niche case and the right side panels (d–f) represent the neutral case. The three layers of panels represent the different magnitudes of change: <i>p = </i>0.1 in the top panels (a, d), <i>p = </i>0.01 in the middle panels (b, e), and <i>p = </i>0 in the bottom panels (c, f). Within each panel, habitat heterogeneity is indicated: <i>k = </i>25 for the upper boxplot and <i>k = </i>4 for the lower boxplot. White boxplots represent the spatial niche case and the grey boxplots represent the neutral case.</p

Several patterns of the frequency distribution for reproductive strategies.

<p>The horizontal axis represents the reproductive strategy (<i>P</i>) of an individual plant (0: seed reproduction only, 1: clonal reproduction only), and the vertical axis represents the frequency of each value of <i>P</i> in the plant population. This depends on the degree of environmental change in a habitat and the number of spatial niches. The number of habitats is fixed at <i>k</i> = 16. The values describing the environmental change for each line are: thick solid line corresponds to (<i>p</i>, <i>q</i>) = (0, 0), solid line with open circles corresponds to (<i>p</i>, <i>q</i>) = (0.01, 0.01), solid line with close circles corresponds to (<i>p</i>, <i>q</i>) = (0.01, 0.1), dotted line with open circles corresponds to (<i>p</i>, <i>q</i>) = (0.1, 0.01), and dashed line with close circles corresponds to (<i>p</i>, <i>q</i>) = (0.1, 0.1).</p

Variables in the model.

<p>Variables in the model.</p

The flow chart for the spatially explicit individual-based simulation of plant dynamics.

<p>The flow chart for the spatially explicit individual-based simulation of plant dynamics.</p

The visual concept of spatial heterogeneity on the habitat lattice and the plant mortality rate

<p>. The figure (a) represents the concept of spatial heterogeneity. The grey scale in the squares represents the trait value (0–1) of the habitat: the value for the pure white habitat is zero and that for the pure black habitat is one. In this case, there are 16 different habitats (<i>E</i>_1,<i>t</i>, <i>E</i>_2,<i>t</i>,…<i>E</i>_16,<i>t</i>) within the total lattice space and each habitat has 2×2 square sites. The grey scale in circles represents the plant trait value (<i>Q</i>_ij). The similarity of the grey scale between <i>E</i>_l,t and <i>Q</i>_ij determines the death rate of the individual plant inhabiting (i, j), and its relationship is illustrated in (b). The two combinations of square and circle are the example of the difference between habitat and plant trait values in (b).</p

Parameters in the model.

<p>Parameters in the model.</p

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population

<div><p>In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant <i>Cardamine leucantha</i>. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.</p></div

Sampling design.

<p>The study plot measured 20 m × 20 m. Vegetation cover data was used as a measure of environmental heterogeneity (a), and the spatial distribution of genets (groups of clonal ramets with shared genotypes) was determined through simple sequence repeat (SSR) analyses (b). In (a), the focal study plot is indicated by red lines. It consisted of four hundred 1-m² quadrats. The vegetation cover of the forest floor (the fraction of the area covered by forest floor herbs and ferns large enough to shade <i>C</i>. <i>leucantha</i> ramets) was classified according to five categories of shading (no shade, ≤ 30%, ≤ 60%, ≤ 90%, or ≤ 100% vegetation cover) for each of the 484 quadrats (the focal 400 plus the surrounding 84). Black dots represent the sampling points. In (b), numbers represent genets, which are numbered in decreasing order of the number of ramets they contained. Patchy and disjunct genet members that belonged to genets with multiple ramets are grouped by shading and circles, respectively. Numbers without shading or circling represent unique genets found in only one sample.</p

Spatial distributions of genet-specific methylation status of four selected loci: Lo2-170 (a), Lo2-292 (b), Lo3-096 (c), and Lo4-075 (d).

<p>Three diagrams for each locus represent n-subepiloci (left), m-subepiloci (middle) and h-subepiloci (right). Symbols as for Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178145#pone.0178145.g001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178145#pone.0178145.g006" target="_blank">6</a>. For statistical details, see the corresponding probability deviance diagrams in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178145#pone.0178145.s007" target="_blank">S3 Fig</a>.</p